Patrick Dorn new ESnet networking engineer


Patrick Dorn bolsters ESnet's midwestern presence

Patrick Dorn has joined ESnet as a network engineer. His responsibilities within the Network Engineering Group will include configuration and management of ESnet devices, internal tool development, and general network engineering duties.

Dorn has more than a decade of experience working with high performance networking in the research and education community.  He comes to ESnet from the National Center for Supercomputing Applications (NCSA), where he served in both technical and management roles. As a network engineer he was technical lead for NCSA’s heterogenous production network as well as primary WAN architect. His activities ranged from supporting I-Wire, a regional optical network, to designing and implementing a self-service “network activation” system for NCSAnet users. Most recently, Dorn was involved with the IP network planning for NCSA’s upcoming Blue Waters supercomputer. As a technical program manager, Dorn supervised NCSA’s network engineering staff and conducted project management and prioritization.

“All of my professional experience has the design and support of production networks at its core,” said Dorn. “The different facets of that experience–from campus LAN and WAN to optical networking to software components such as DNS–give me a broad foundation to evaluate new technologies. I’m excited about the ESnet opportunity because it offers challenges of scale along a number of different axes: performance, scope, and complexity.”

A veteran SCinet Committee member, Dorn has served on multiple engineering teams to set up the complex temporary network that supports the SC conference series. As the 2008 SCinet Chair, he led the SCinet effort in Austin, TX. Dorn has also lectured on IP multicast deployment and troubleshooting.

A native of Springfield, IL, Dorn received his bachelor of science in computer engineering from the University of Illinois at Urbana-Champaign.  Dorn is an avid college basketball fan and enjoys traveling. He is also an architecture buff– and is partial to the work of Frank Lloyd Wright. Coincidentally, Dorn will be based in Illinois, the mecca for Wright–influenced architecture.

I.T. in-depth at DUSEL


This guest blog is contributed by Warren Matthews, Cyber-Infrastructure Chief Engineer at the Deep Underground Science and Engineering Lab (DUSEL).
 

Guest Blogger: Warren Matthews, DUSEL

The Deep Underground Science and Engineering Laboratory (DUSEL) is a research lab being constructed in the former Homestake gold mine in Lead, South Dakota, now resurrected to mine data about the earth, new life forms, and the universe itself. When finished, DUSEL will explore fundamental questions in particle physics, nuclear physics and astrophysics. Biologists will study life in extreme environments. Geologists will study the structure of the earth’s crust. Early science programs have already begun to explore some of these questions. In addition, DUSEL education programs are underway to inspire students to pursue careers in science, technology, engineering, and mathematics. This interdisciplinary collaboration of scientists and engineers is led by the University of California at Berkeley and the South Dakota School of Mines and Technology.

 

I am the cyberinfrastructure chief engineer for DUSEL. As such, my concern is the research environment and advanced services that will be needed to accomplish our scientific goals. To enable future discoveries, scientists will need to capture, analyze, and exchange their data. We will have to deploy and perhaps even develop new technologies to provide the scientists with the technical and logistical support for their research. We expect that the unique research opportunities and instrumentation that will be established at DUSEL will draw scientific teams from all over the world to South Dakota, so high-speed national and International network connectivity will also critical.

National laboratories have made many important contributions in the development of IT and networking technology.  I’m very pleased that DUSEL is the newest member of the ESnet community and I have no doubt that we’ll be leveraging their expertise.  In conversations with numerous colleagues at other labs it has become apparent that although DUSEL is starting with a clean slate and there are no legacy systems to support, we still have common issues and some difficult decisions to consider. All the labs have the challenges of meeting the needs of both large and small scientific collaborations. We all feel the budget crunch and are streamlining our support infrastructure. We are all wondering how we can optimize our use of the Cloud.

Delving into underground research

At DUSEL we have our own particular challenges, starting with an extreme underground environment. On the surface, the Black Hills of South Dakota may be freezing, but the further you go down in the mine, the hotter it gets. Rock temperatures at the 4850′ level, where the mid-level campus is under construction, are around 70F (21〫C) and humidity is around 88%. At the 7400′ level, where the deep-level campus is planned, temperatures hover around 120F (50〫C). The high levels of temperature and humidity have a significant impact on computer equipment.  We’ll figure out our challenges as we go, depending on shared expertise. After all, national labs were created to focus effort and move forward knowledge where no one university could marshal the resources required. Our goal is to provide a platform where science, technology, and innovation are able to flourish.

We anticipate technology partnerships with the many experiments are going underground at DUSEL. Currently we are expanding IPv6 and deploying perfSONAR. We are leveraging HD video conferencing. We are worrying about identity management and cyber security. We are establishing the requirements for dynamic network provisioning.  And at the same time we’re wondering what other technologies will emerge in the next 20 or 30 years and what will be required to dig for new discoveries. You can keep track of our progress here at the Sanford Laboratory Youtube Channel.

–Warren Matthews

Harnessing bugs for new drugs and potential jet fuel


D. radiodurans is impervious to ionizing radiation; can clean up mercury and toluene contamination

The high speed networking that ESnet provides supports an incredibly varied range of scientific projects. The express purpose of DOE national labs is to conduct research in the national interest. Much is basic research, exploring fundamental issue in physics, energy, cosmology, and climate science. However the study of microbial evolution is one intriguing area that is already changing our lives with everything from new medicines to potential fuels.

Microbes are single-cell organisms that live in colonies and can be found in nearly every corner of our planet, in places ranging from insects’ intestines to some of the most toxic chemical environments. The site for the most detailed information on the genetic makeup of these organisms only lives in one place – at the DOE’s Joint Genome Institute – and is accessed via ESnet.  The Integrated Microbial Genomes (IMG) Data Management System provides the genetic makeup of thousands of microbes and tools for analyzing the functional capability of microbial communities based on their metagenome DNA sequence. Understanding these tiny organisms can provide new insights into a wide range of important problems, but in order to study the microbes, scientists need reliable access to the genomic data.

Microbes such as bacteria are responsible for a number of diseases, such as plague, tuberculosis and anthrax, while microbes known as protozoa cause diseases such as malaria, sleeping sickness and toxoplasmosis. On the plus side, microbes also live helpfully in human digestive systems, helping to digest carbohydrates and synthesize certain vitamins.

Where the wild things are

Famously, taq polymerase, an enzyme isolated from the bacterium Thermus aquaticus found in a hot spring at Yellowstone National Park in 1965, became the basis for PCR, the technique for amplifying short strands of DNA that has revolutionized biologic and genetic research. While some scientists examine exotic microbes like Deinococcus radiodurans, the most radiation-resistant organism known (and the darling of exobiologists, found as a contaminant of irradiated canned meat in 1956) for clues to how life began on earth and could evolve on other planets, your laundry detergent probably contains enzymes developed from bacteria that evolved in hot, alkaline conditions.

In the private sector, microbes are genetically modified to develop innovative drugs as well as industrial products. In an example close to home, a few years back, LBNL’s Joint BioEnergy Institute director Jay Keasling used microbial evolution techniques to synthesize artemisinic acid, a precursor to artemisinin, an anti-malarial compound. Artemisinin is derived from Artemisia annua or wormwood, a plant known to Chinese medicine for centuries. Keasling made a steady supply that could be manufactured extremely cheaply and at large volumes, so accessible to people in developing countries.

Keasling’s next project is to use microbes as potential energy sources by turning them into factories to produce sugars. Certain microbes living in termite guts are essential for digesting the wood fibers eaten by the insect. While this can be bad news for homeowners, the chemical capabilities of the “bugs” in these bugs are being studied as for their potential in converting wood and other plant matter into new energy sources. Successfully producing fuel using plant waste instead of food crops like corn, could improve our country’s future energy options.  To be sure, there still are prosaic bars to overcome, such as chemical separation and processing in volumes high enough to meet our insatiable demand for transport fuels. Other scientists at DOE national labs such as NREL and a host of private companies, some right across San Francisco Bay from our headquarters at ESnet, are investigating how to make gasoline and jet fuel from microorganisms. Genetic analysis is the essential first step in growing hardworking bacteria with the desired qualities.

Another promising microbial application is environmental cleanup. One form of bacteria found almost 2 miles underground in a South African gold mine lives in total darkness, 140 degrees Fahrenheit – and no oxygen. The organism gets its energy not from the sun but from hydrogen and sulfate produced by the radioactive decay of uranium. By understanding how life can thrive in such an apparently toxic setting, scientists may get new insight into using microbes to clean up environmental contamination.

Currently, the IMG database contains complete genomes for 4,879 microbes, with another 1,569 in draft form. Of the total, 1,107 are bacteria and 2,536 are viruses. The information, containing data for more than 20 million genes, is provided freely to interested researchers.